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        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        About MultiQC

        This report was generated using MultiQC, version 1.11 (72e575d)

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        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2022-07-19, 18:16 based on data in: /scratch1/users/dadras/response_to_gradient_of_environmental_cues_in_mesotaenium


        General Statistics

        Showing 263/263 rows and 7/9 columns.
        Sample Name# VariantsFrag Length% AlignedM Aligned% Dups% GCM Seqs
        BR_1_13_1
        254.2bp
        87.9%
        24.9
        71.3%
        54%
        29.0
        BR_1_13_2
        73.2%
        54%
        29.0
        BR_1_19_1
        250.7bp
        85.9%
        28.8
        70.2%
        55%
        35.2
        BR_1_19_2
        70.3%
        56%
        35.2
        BR_1_25_1
        253.5bp
        86.1%
        29.3
        70.6%
        54%
        34.9
        BR_1_25_2
        72.5%
        54%
        34.9
        BR_1_31_1
        258.5bp
        84.9%
        25.6
        69.5%
        54%
        30.9
        BR_1_31_2
        70.7%
        54%
        30.9
        BR_1_35_1
        262.3bp
        88.2%
        27.4
        72.4%
        54%
        31.8
        BR_1_35_2
        74.2%
        54%
        31.8
        BR_1_8_1
        277.2bp
        88.9%
        28.2
        83.2%
        54%
        32.6
        BR_1_8_2
        83.5%
        54%
        32.6
        BR_2_13_1
        246.2bp
        86.0%
        34.5
        71.5%
        55%
        41.8
        BR_2_13_2
        72.2%
        56%
        41.8
        BR_2_19_1
        265.9bp
        86.9%
        29.8
        71.9%
        54%
        35.1
        BR_2_19_2
        73.8%
        54%
        35.1
        BR_2_25_1
        266.5bp
        86.4%
        28.5
        72.7%
        54%
        33.8
        BR_2_25_2
        74.4%
        54%
        33.8
        BR_2_8_1
        245.3bp
        87.5%
        33.5
        67.4%
        55%
        40.0
        BR_2_8_2
        68.8%
        56%
        40.0
        BR_3_13_1
        237.2bp
        86.8%
        30.2
        69.0%
        55%
        36.4
        BR_3_13_2
        69.4%
        56%
        36.4
        BR_3_19_1
        245.1bp
        86.7%
        29.4
        66.4%
        55%
        35.4
        BR_3_19_2
        67.6%
        55%
        35.4
        BR_3_25_1
        239.5bp
        85.0%
        26.5
        65.0%
        55%
        32.6
        BR_3_25_2
        65.4%
        56%
        32.6
        BR_3_31_1
        242.6bp
        83.6%
        24.6
        63.2%
        55%
        30.8
        BR_3_31_2
        63.2%
        56%
        30.8
        BR_3_35_1
        245.1bp
        87.7%
        29.3
        67.1%
        55%
        34.9
        BR_3_35_2
        67.6%
        55%
        34.9
        BR_3_8_1
        248.8bp
        88.0%
        27.8
        68.3%
        55%
        32.9
        BR_3_8_2
        69.1%
        55%
        32.9
        B_1_10_1
        200.9bp
        89.4%
        29.0
        67.2%
        55%
        33.2
        B_1_10_2
        71.8%
        55%
        33.2
        B_1_11_1
        252.3bp
        89.4%
        38.2
        68.9%
        55%
        43.8
        B_1_11_2
        74.3%
        56%
        43.8
        B_1_12_1
        256.2bp
        90.0%
        33.6
        69.8%
        55%
        38.2
        B_1_12_2
        74.2%
        55%
        38.2
        B_1_13_1
        271.6bp
        79.9%
        24.0
        63.9%
        55%
        30.9
        B_1_13_2
        67.9%
        55%
        30.9
        B_1_14_1
        232.1bp
        88.1%
        38.9
        68.7%
        55%
        45.2
        B_1_14_2
        73.9%
        55%
        45.2
        B_1_15_1
        232.5bp
        89.4%
        43.3
        72.3%
        55%
        49.6
        B_1_15_2
        77.8%
        55%
        49.6
        B_1_16_1
        256.4bp
        89.9%
        35.9
        70.9%
        55%
        41.0
        B_1_16_2
        75.3%
        55%
        41.0
        B_1_17_1
        211.3bp
        89.9%
        36.0
        71.7%
        54%
        41.0
        B_1_17_2
        76.5%
        55%
        41.0
        B_1_18_1
        226.1bp
        89.5%
        28.9
        69.8%
        55%
        33.0
        B_1_18_2
        74.1%
        56%
        33.0
        B_1_19_1
        250.6bp
        87.6%
        30.6
        68.2%
        55%
        35.8
        B_1_19_2
        72.9%
        56%
        35.8
        B_1_20_1
        211.6bp
        87.9%
        28.0
        65.5%
        55%
        32.7
        B_1_20_2
        69.7%
        56%
        32.7
        B_1_21_1
        262.5bp
        89.0%
        29.6
        68.4%
        55%
        34.2
        B_1_21_2
        72.2%
        56%
        34.2
        B_1_22_1
        254.8bp
        89.6%
        31.2
        68.2%
        55%
        35.7
        B_1_22_2
        72.6%
        56%
        35.7
        B_1_23_1
        244.4bp
        89.2%
        29.4
        66.8%
        56%
        33.9
        B_1_23_2
        70.9%
        56%
        33.9
        B_1_24_1
        236.5bp
        89.0%
        29.1
        69.6%
        55%
        33.5
        B_1_24_2
        74.1%
        56%
        33.5
        B_1_25_1
        282.1bp
        65.2%
        25.4
        67.2%
        53%
        40.0
        B_1_25_2
        71.1%
        54%
        40.0
        B_1_26_1
        264.2bp
        88.0%
        29.7
        65.9%
        56%
        34.7
        B_1_26_2
        70.2%
        56%
        34.7
        B_1_27_1
        241.6bp
        88.3%
        33.7
        73.5%
        56%
        39.2
        B_1_27_2
        78.1%
        56%
        39.2
        B_1_28_1
        271.3bp
        81.9%
        33.9
        73.3%
        55%
        42.5
        B_1_28_2
        77.5%
        55%
        42.5
        B_1_29_1
        270.6bp
        87.7%
        34.9
        70.7%
        55%
        40.7
        B_1_29_2
        75.1%
        55%
        40.7
        B_1_30_1
        262.7bp
        89.6%
        35.8
        69.7%
        55%
        40.9
        B_1_30_2
        74.6%
        56%
        40.9
        B_1_31_1
        221.9bp
        82.5%
        25.7
        72.5%
        56%
        32.5
        B_1_31_2
        71.8%
        57%
        32.5
        B_1_32_1
        242.9bp
        85.9%
        38.9
        71.6%
        55%
        47.0
        B_1_32_2
        72.6%
        56%
        47.0
        B_1_33_1
        211.1bp
        86.3%
        34.5
        73.5%
        55%
        41.7
        B_1_33_2
        73.1%
        56%
        41.7
        B_1_34_1
        175.9bp
        86.8%
        8.0
        50.1%
        56%
        9.5
        B_1_34_2
        51.1%
        56%
        9.5
        B_1_35_1
        183.4bp
        86.6%
        25.8
        70.8%
        55%
        30.8
        B_1_35_2
        72.5%
        55%
        30.8
        B_1_36_1
        243.0bp
        88.2%
        50.1
        77.0%
        55%
        59.1
        B_1_36_2
        77.0%
        55%
        59.1
        B_1_38_1
        220.8bp
        84.0%
        26.5
        65.9%
        56%
        32.7
        B_1_38_2
        66.9%
        56%
        32.7
        B_1_39_1
        197.9bp
        84.9%
        27.3
        70.9%
        56%
        33.5
        B_1_39_2
        68.4%
        57%
        33.5
        B_1_3_1
        239.5bp
        88.7%
        34.6
        69.9%
        55%
        39.9
        B_1_3_2
        74.4%
        56%
        39.9
        B_1_40_1
        252.0bp
        86.0%
        31.7
        63.9%
        56%
        38.4
        B_1_40_2
        63.7%
        56%
        38.4
        B_1_41_1
        215.2bp
        86.1%
        34.8
        65.1%
        55%
        41.8
        B_1_41_2
        65.8%
        56%
        41.8
        B_1_42_1
        191.1bp
        86.1%
        32.0
        67.1%
        55%
        38.5
        B_1_42_2
        68.6%
        55%
        38.5
        B_1_4_1
        224.6bp
        88.6%
        30.4
        67.8%
        55%
        35.1
        B_1_4_2
        72.5%
        56%
        35.1
        B_1_5_1
        214.8bp
        89.4%
        40.9
        69.7%
        55%
        47.0
        B_1_5_2
        75.3%
        55%
        47.0
        B_1_6_1
        247.7bp
        89.2%
        35.4
        68.4%
        55%
        40.8
        B_1_6_2
        72.8%
        56%
        40.8
        B_1_8_1
        240.8bp
        86.3%
        30.9
        77.0%
        55%
        36.7
        B_1_8_2
        80.7%
        55%
        36.7
        B_1_9_1
        247.5bp
        89.7%
        37.6
        69.5%
        55%
        42.9
        B_1_9_2
        74.6%
        55%
        42.9
        B_2_10_1
        257.4bp
        89.0%
        38.1
        70.2%
        55%
        44.2
        B_2_10_2
        70.7%
        55%
        44.2
        B_2_11_1
        256.0bp
        89.6%
        28.4
        67.9%
        55%
        32.7
        B_2_11_2
        68.5%
        56%
        32.7
        B_2_12_1
        311.3bp
        89.6%
        31.4
        70.3%
        55%
        36.6
        B_2_12_2
        68.1%
        56%
        36.6
        B_2_13_1
        197.3bp
        85.5%
        24.5
        66.1%
        56%
        29.6
        B_2_13_2
        66.8%
        56%
        29.6
        B_2_14_1
        265.2bp
        87.9%
        36.1
        75.0%
        55%
        42.5
        B_2_14_2
        74.3%
        56%
        42.5
        B_2_15_1
        250.3bp
        88.7%
        30.8
        68.9%
        55%
        35.9
        B_2_15_2
        69.4%
        56%
        35.9
        B_2_16_1
        217.9bp
        88.9%
        36.4
        74.4%
        55%
        42.2
        B_2_16_2
        74.5%
        55%
        42.2
        B_2_17_1
        200.2bp
        89.7%
        33.0
        74.2%
        54%
        37.9
        B_2_17_2
        74.6%
        54%
        37.9
        B_2_18_1
        246.2bp
        89.5%
        28.8
        69.5%
        55%
        33.2
        B_2_18_2
        70.3%
        55%
        33.2
        B_2_19_1
        199.9bp
        86.3%
        26.4
        70.9%
        55%
        31.8
        B_2_19_2
        70.2%
        56%
        31.8
        B_2_20_1
        251.5bp
        88.7%
        26.3
        65.6%
        54%
        30.9
        B_2_20_2
        65.2%
        55%
        30.9
        B_2_21_1
        248.7bp
        89.4%
        28.8
        69.9%
        55%
        33.3
        B_2_21_2
        70.2%
        55%
        33.3
        B_2_22_1
        219.8bp
        88.2%
        30.2
        71.0%
        55%
        35.3
        B_2_22_2
        71.4%
        55%
        35.3
        B_2_23_1
        236.0bp
        89.0%
        31.0
        71.0%
        55%
        35.9
        B_2_23_2
        71.4%
        55%
        35.9
        B_2_24_1
        265.1bp
        89.6%
        29.7
        73.8%
        55%
        34.3
        B_2_24_2
        72.9%
        56%
        34.3
        B_2_25_1
        242.7bp
        84.7%
        32.9
        77.0%
        56%
        40.3
        B_2_25_2
        76.2%
        56%
        40.3
        B_2_26_1
        199.3bp
        86.7%
        25.8
        71.3%
        55%
        30.9
        B_2_26_2
        70.3%
        55%
        30.9
        B_2_27_1
        237.8bp
        87.9%
        26.3
        69.3%
        55%
        31.0
        B_2_27_2
        69.3%
        56%
        31.0
        B_2_28_1
        218.4bp
        87.4%
        27.5
        71.4%
        55%
        32.6
        B_2_28_2
        71.9%
        56%
        32.6
        B_2_29_1
        248.3bp
        88.5%
        31.0
        69.7%
        55%
        36.1
        B_2_29_2
        69.8%
        55%
        36.1
        B_2_30_1
        232.1bp
        87.9%
        33.8
        71.9%
        55%
        39.8
        B_2_30_2
        71.9%
        55%
        39.8
        B_2_31_1
        251.0bp
        84.2%
        26.9
        64.8%
        56%
        33.4
        B_2_31_2
        63.8%
        56%
        33.4
        B_2_32_1
        203.0bp
        83.3%
        23.9
        65.5%
        55%
        29.8
        B_2_32_2
        66.5%
        56%
        29.8
        B_2_33_1
        253.1bp
        87.2%
        29.9
        65.2%
        55%
        35.5
        B_2_33_2
        65.4%
        56%
        35.5
        B_2_34_1
        230.3bp
        87.7%
        26.9
        66.0%
        55%
        31.7
        B_2_34_2
        66.0%
        56%
        31.7
        B_2_35_1
        230.7bp
        87.5%
        27.6
        65.8%
        56%
        32.7
        B_2_35_2
        66.0%
        56%
        32.7
        B_2_36_1
        231.8bp
        87.6%
        28.4
        71.2%
        55%
        33.4
        B_2_36_2
        72.8%
        55%
        33.4
        B_2_38_1
        242.2bp
        80.2%
        28.1
        72.5%
        55%
        36.3
        B_2_38_2
        71.3%
        56%
        36.3
        B_2_39_1
        201.2bp
        87.1%
        28.9
        75.8%
        51%
        34.2
        B_2_39_2
        75.0%
        52%
        34.2
        B_2_3_1
        259.4bp
        84.9%
        29.6
        66.6%
        55%
        36.1
        B_2_3_2
        66.8%
        55%
        36.1
        B_2_40_1
        200.3bp
        85.0%
        32.0
        65.1%
        55%
        38.9
        B_2_40_2
        65.8%
        55%
        38.9
        B_2_41_1
        251.5bp
        85.5%
        24.8
        61.9%
        56%
        30.0
        B_2_41_2
        62.3%
        56%
        30.0
        B_2_42_1
        212.3bp
        86.2%
        33.7
        65.9%
        55%
        40.3
        B_2_42_2
        66.9%
        56%
        40.3
        B_2_4_1
        248.1bp
        89.3%
        27.6
        67.8%
        55%
        31.8
        B_2_4_2
        68.0%
        55%
        31.8
        B_2_5_1
        253.8bp
        89.1%
        36.9
        70.9%
        55%
        42.8
        B_2_5_2
        71.0%
        55%
        42.8
        B_2_6_1
        253.2bp
        89.1%
        35.9
        70.1%
        55%
        41.8
        B_2_6_2
        69.8%
        55%
        41.8
        B_2_8_1
        255.2bp
        88.5%
        32.8
        67.8%
        55%
        38.6
        B_2_8_2
        67.8%
        56%
        38.6
        B_2_9_1
        260.7bp
        88.9%
        32.7
        69.0%
        55%
        38.2
        B_2_9_2
        69.1%
        56%
        38.2
        B_3_10_1
        223.8bp
        90.0%
        30.3
        70.9%
        54%
        34.7
        B_3_10_2
        71.5%
        55%
        34.7
        B_3_11_1
        258.7bp
        89.3%
        50.2
        77.4%
        55%
        58.5
        B_3_11_2
        77.5%
        55%
        58.5
        B_3_12_1
        226.3bp
        88.7%
        34.7
        71.2%
        55%
        40.0
        B_3_12_2
        75.8%
        55%
        40.0
        B_3_13_1
        236.2bp
        87.3%
        37.7
        70.1%
        56%
        44.3
        B_3_13_2
        75.5%
        56%
        44.3
        B_3_14_1
        246.4bp
        89.5%
        37.3
        68.2%
        55%
        42.7
        B_3_14_2
        73.5%
        55%
        42.7
        B_3_15_1
        265.3bp
        88.5%
        40.3
        74.2%
        55%
        47.2
        B_3_15_2
        74.5%
        56%
        47.2
        B_3_16_1
        236.5bp
        89.8%
        36.6
        69.1%
        55%
        41.8
        B_3_16_2
        74.1%
        55%
        41.8
        B_3_17_1
        232.9bp
        90.2%
        36.3
        70.3%
        55%
        41.1
        B_3_17_2
        75.5%
        55%
        41.1
        B_3_18_1
        242.2bp
        89.7%
        40.7
        70.0%
        55%
        46.5
        B_3_18_2
        75.2%
        56%
        46.5
        B_3_19_1
        216.5bp
        86.9%
        34.5
        66.7%
        56%
        40.8
        B_3_19_2
        71.4%
        56%
        40.8
        B_3_20_1
        227.8bp
        88.4%
        40.6
        69.7%
        55%
        47.1
        B_3_20_2
        74.8%
        56%
        47.1
        B_3_21_1
        221.0bp
        88.8%
        38.3
        69.3%
        55%
        44.2
        B_3_21_2
        74.5%
        56%
        44.2
        B_3_22_1
        253.9bp
        90.1%
        37.1
        70.6%
        55%
        42.2
        B_3_22_2
        74.9%
        55%
        42.2
        B_3_23_1
        254.1bp
        88.7%
        38.0
        72.0%
        55%
        44.0
        B_3_23_2
        76.5%
        56%
        44.0
        B_3_24_1
        259.8bp
        89.3%
        33.0
        69.1%
        55%
        37.9
        B_3_24_2
        73.4%
        56%
        37.9
        B_3_25_1
        235.2bp
        85.5%
        32.3
        65.2%
        56%
        38.6
        B_3_25_2
        70.4%
        56%
        38.6
        B_3_26_1
        243.5bp
        88.3%
        33.0
        66.6%
        55%
        38.4
        B_3_26_2
        71.2%
        56%
        38.4
        B_3_27_1
        227.0bp
        88.9%
        37.1
        68.5%
        55%
        42.9
        B_3_27_2
        73.3%
        55%
        42.9
        B_3_28_1
        250.3bp
        88.8%
        34.2
        68.7%
        55%
        39.4
        B_3_28_2
        73.6%
        56%
        39.4
        B_3_29_1
        209.5bp
        88.7%
        37.0
        69.5%
        55%
        42.8
        B_3_29_2
        74.3%
        55%
        42.8
        B_3_30_1
        246.2bp
        88.4%
        33.8
        69.4%
        55%
        39.2
        B_3_30_2
        73.8%
        56%
        39.2
        B_3_31_1
        242.5bp
        84.7%
        35.5
        64.6%
        55%
        43.0
        B_3_31_2
        69.7%
        56%
        43.0
        B_3_32_1
        275.9bp
        78.2%
        37.1
        65.0%
        56%
        48.6
        B_3_32_2
        69.2%
        56%
        48.6
        B_3_33_1
        230.5bp
        87.0%
        30.3
        65.1%
        56%
        35.8
        B_3_33_2
        69.5%
        56%
        35.8
        B_3_34_1
        224.1bp
        88.4%
        34.1
        66.6%
        55%
        39.6
        B_3_34_2
        71.5%
        56%
        39.6
        B_3_35_1
        247.8bp
        88.8%
        32.0
        66.2%
        55%
        37.0
        B_3_35_2
        70.5%
        56%
        37.0
        B_3_36_1
        211.3bp
        87.1%
        33.0
        65.3%
        56%
        38.7
        B_3_36_2
        70.1%
        56%
        38.7
        B_3_38_1
        201.5bp
        82.0%
        26.3
        61.6%
        54%
        33.3
        B_3_38_2
        62.2%
        55%
        33.3
        B_3_39_1
        245.5bp
        86.9%
        36.1
        63.6%
        55%
        42.7
        B_3_39_2
        67.9%
        56%
        42.7
        B_3_3_1
        214.5bp
        88.3%
        27.3
        65.9%
        55%
        31.9
        B_3_3_2
        66.7%
        55%
        31.9
        B_3_40_1
        224.7bp
        86.6%
        36.0
        62.9%
        55%
        42.6
        B_3_40_2
        67.7%
        56%
        42.6
        B_3_41_1
        244.7bp
        87.2%
        35.9
        64.9%
        55%
        42.3
        B_3_41_2
        69.5%
        56%
        42.3
        B_3_42_1
        243.0bp
        87.5%
        43.1
        66.7%
        55%
        50.4
        B_3_42_2
        72.3%
        56%
        50.4
        B_3_4_1
        210.2bp
        88.7%
        31.4
        68.6%
        55%
        36.5
        B_3_4_2
        68.9%
        55%
        36.5
        B_3_5_1
        212.7bp
        88.6%
        30.3
        68.1%
        55%
        35.3
        B_3_5_2
        69.2%
        55%
        35.3
        B_3_6_1
        216.6bp
        88.6%
        36.7
        69.7%
        55%
        42.9
        B_3_6_2
        70.5%
        55%
        42.9
        B_3_8_1
        239.3bp
        88.7%
        34.3
        70.4%
        55%
        40.1
        B_3_8_2
        70.6%
        55%
        40.1
        B_3_9_1
        258.5bp
        89.1%
        31.3
        72.5%
        55%
        36.4
        B_3_9_2
        72.7%
        56%
        36.4
        multiqc
        0
        re_B_1_34_1
        248.3bp
        84.1%
        21.2
        65.8%
        56%
        26.1
        re_B_1_34_2
        66.4%
        56%
        26.1

        Snippy

        Snippy is used for rapid haploid variant calling and core genome alignment.

        Snippy Variants

        This plot shows the different variant types reported by snippy.

        Error - was not able to plot data.


        Kallisto

        Kallisto is a program for quantifying abundances of transcripts from RNA-Seq data.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        FastQC

        FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.

        Sequence Counts

        Sequence counts for each sample. Duplicate read counts are an estimate only.

        This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

        You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Quality Histograms

        The mean quality value across each base position in the read.

        To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

        Taken from the FastQC help:

        The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Sequence Quality Scores

        The number of reads with average quality scores. Shows if a subset of reads has poor quality.

        From the FastQC help:

        The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Base Sequence Content

        The proportion of each base position for which each of the four normal DNA bases has been called.

        To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

        To see the data as a line plot, as in the original FastQC graph, click on a sample track.

        From the FastQC help:

        Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

        In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

        It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

        Click a sample row to see a line plot for that dataset.
        Rollover for sample name
        Position: -
        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

        From the FastQC help:

        This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

        In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

        An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Base N Content

        The percentage of base calls at each position for which an N was called.

        From the FastQC help:

        If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

        It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Length Distribution

        All samples have sequences of a single length (150bp).

        Sequence Duplication Levels

        The relative level of duplication found for every sequence.

        From the FastQC Help:

        In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (eg PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Overrepresented sequences

        The total amount of overrepresented sequences found in each library.

        FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as over represented.

        Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

        From the FastQC Help:

        A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

        FastQC lists all of the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Adapter Content

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

        Note that only samples with ≥ 0.1% adapter contamination are shown.

        There may be several lines per sample, as one is shown for each adapter detected in the file.

        From the FastQC Help:

        The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Status Checks

        Status for each FastQC section showing whether results seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        FastQC assigns a status for each section of the report. These give a quick evaluation of whether the results of the analysis seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        It is important to stress that although the analysis results appear to give a pass/fail result, these evaluations must be taken in the context of what you expect from your library. A 'normal' sample as far as FastQC is concerned is random and diverse. Some experiments may be expected to produce libraries which are biased in particular ways. You should treat the summary evaluations therefore as pointers to where you should concentrate your attention and understand why your library may not look random and diverse.

        Specific guidance on how to interpret the output of each module can be found in the relevant report section, or in the FastQC help.

        In this heatmap, we summarise all of these into a single heatmap for a quick overview. Note that not all FastQC sections have plots in MultiQC reports, but all status checks are shown in this heatmap.

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